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VEBER Philippe
codepi
Commits
f3ec331f
Commit
f3ec331f
authored
Nov 22, 2020
by
Philippe Veber
Browse files
tk/Tdg09: expose default implementation
parent
87b4f2e6
Changes
2
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2 changed files
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28 additions
and
6 deletions
+28
-6
lib/tk/tdg09.ml
lib/tk/tdg09.ml
+8
-2
lib/tk/tdg09.mli
lib/tk/tdg09.mli
+20
-4
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lib/tk/tdg09.ml
View file @
f3ec331f
...
...
@@ -417,10 +417,12 @@ module Make(Branch_info : Branch_info)(Leaf_info : Leaf_info)(Site : Site with t
end
end
module
Implementation_check
=
struct
module
Pack
=
struct
type
leaf_info
=
int
*
Convergence_tree
.
condition
module
Leaf_info
=
struct
type
species
=
int
type
t
=
species
*
Convergence_tree
.
condition
type
t
=
leaf_info
let
condition
=
snd
let
species
=
fst
end
...
...
@@ -451,6 +453,10 @@ module Implementation_check = struct
|>
branch
branch_length1
`Ancestral
in
Tree
.
node
()
(
List1
.
init
npairs
~
f
:
make_pair
)
end
module
Implementation_check
=
struct
open
Pack
let
likelihood_plot_demo
(
wag
:
Wag
.
t
)
=
let
tree
=
pair_tree
~
branch_length1
:
1
.
~
branch_length2
:
1
.
~
npairs
:
100
in
...
...
lib/tk/tdg09.mli
View file @
f3ec331f
...
...
@@ -124,13 +124,29 @@ module Make(Branch_info : Branch_info)(Leaf_info : Leaf_info)(Site : Site with t
and
type
leaf_info
:=
Leaf_info
.
t
and
type
branch_info
:=
Branch_info
.
t
module
Implementation_check
:
sig
include
S
with
type
site
:=
Amino_acid
.
t
array
and
type
leaf_info
:=
int
*
Convergence_tree
.
condition
and
type
branch_info
:=
Convergence_tree
.
Branch_info
.
t
module
Pack
:
sig
type
leaf_info
=
int
*
Convergence_tree
.
condition
module
Leaf_info
:
Leaf_info
with
type
t
=
leaf_info
and
type
species
=
int
module
Site
:
Site
with
type
species
=
int
and
type
t
=
Amino_acid
.
t
array
include
module
type
of
Make
(
Convergence_tree
.
Branch_info
)(
Leaf_info
)(
Site
)
val
simulate_profile
:
float
->
Amino_acid
.
vector
val
pair_tree
:
branch_length1
:
float
->
branch_length2
:
float
->
npairs
:
int
->
(
unit
,
leaf_info
,
Convergence_tree
.
branch_info
)
Tree
.
t
end
module
Implementation_check
:
sig
open
Pack
val
likelihood_plot_demo
:
Wag
.
t
->
unit
val
lrt_1_vs_2_null_simulation
:
...
...
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